It was at 04.30 local time on Wednesday that contact was broken with the submarine Kri Nanggala 402, 9.5 km north of the island of Bali in Indonesia.
The submarine, which was part of a military exercise, was to rehearse before a sharp torpedo exercise when the officer asked to dive.
According to Indonesia's Defense Ministry, permission was granted - after which contact was lost.
On Wednesday, a massive search effort was underway.
According to the country's military chief Hadi Tjahjanto, several ships have been mobilized in the area.
The country has also turned to Singapore and Australia, which have rescue submarines, for help.
The Indian Ministry of Defense has also been contacted, according to Reuters.
Oil spill found
During the day, a helicopter encountered oil spills on the sea surface at the position where the submarine was most recently located.
But on Wednesday night, the submarine had not yet been found.
The Indonesian military has said that an electrical fault is believed to have occurred in connection with the dive, which has thus resulted in lost control of the submarine and made emergency calls impossible.
It is also stated that the submarine probably sank to a depth of between 600-700 meters, according to AP.
The submarine was built in Germany and has been in use in Indonesia since 1981.
The 53-man crew on board consisted of 49 sailors, three shooters and an officer.